The Remove from Project command in the Project menu closes the active file and removes it from the project. For unmanaged projects, there is no difference between Project|Remove from Project and File|Close. For managed projects, files closed with Project|Remove from Project are completely removed from the project, while files closed with File|Close remain part of the project if they were added to the project.
If you want to remove a file that is already closed from a managed project, use the Files Panel. If you want to remove all closed files from a managed project, use Project|Remove Closed Files. If you want to remove all outside files from a project, use Project|Close Outside Files.
Files that are removed from a project are added to the File|Open and Project|Add to Project submenus that list recently closed files, unless the files were opened in bulk with Project|Open Folder or a similar command.
Project|Remove Closed Files
Project|Remove Obsolete Files
Project|Close Outside Files
Project|Close All Files